FastQC Summary

Summary statistics for all libraries
Filename Total Flagged As Poor Quality Sequence Length %GC
A_1.fq.gz 45,784,482 0 150-150 47
A_2.fq.gz 45,784,482 0 150-150 47
D_1.fq.gz 47,700,555 0 150-150 46
D_2.fq.gz 47,700,555 0 150-150 47
G_1.fq.gz 48,183,768 0 150-150 47
G_2.fq.gz 48,183,768 0 150-150 47
L_1.fq.gz 41,997,745 0 150-150 47
L_2.fq.gz 41,997,745 0 150-150 47
S2_1.fq.gz 44,968,804 0 150-150 47
S2_2.fq.gz 44,968,804 0 150-150 47
S4_1.fq.gz 43,364,251 0 150-150 47
S4_2.fq.gz 43,364,251 0 150-150 47
S5_1.fq.gz 43,177,450 0 150-150 47
S5_2.fq.gz 43,177,450 0 150-150 48
S8_1.fq.gz 43,700,910 0 150-150 46
S8_2.fq.gz 43,700,910 0 150-150 47

Read Totals

Library Sizes ranged between 41,997,745 and 48,183,768 reads.

Read totals for each library. Duplicated reads are conventionally an high overestimate at this point.

FastQC Summary

Summary of FastQC flags for each parameter

Per Base Sequence Quality

Heatmap showing mean base qualities for each library

Per Sequence Quality Scores

Heatmap showing mean sequence qualities for each library

Per Base Sequence Content

Heatmap of summed base distributions along each read

Per Sequence GC Content

GC Content Heatmap normalised to theoretical GC content in the Drerio Transcriptome

GC Content Distributions for all reads showing theoretical GC content from the Drerio Transcriptome

Sequence Length Distribution

Sequence Duplication Levels

Adapter Content

Universal Adapter Content

Overrepresented Summary

Total overrepresented sequences for each library

Overrepresented Sequences

## Overrepresented_sequences missing from A_1.fq.gz
## Overrepresented_sequences missing from A_2.fq.gz
## Overrepresented_sequences missing from D_1.fq.gz
## Overrepresented_sequences missing from D_2.fq.gz
## Overrepresented_sequences missing from G_1.fq.gz
## Overrepresented_sequences missing from G_2.fq.gz
## Overrepresented_sequences missing from L_1.fq.gz
## Overrepresented_sequences missing from L_2.fq.gz
## Overrepresented_sequences missing from S2_1.fq.gz
## Overrepresented_sequences missing from S2_2.fq.gz
## Overrepresented_sequences missing from S4_1.fq.gz
## Overrepresented_sequences missing from S4_2.fq.gz
## Overrepresented_sequences missing from S5_1.fq.gz
## Overrepresented_sequences missing from S5_2.fq.gz
## Overrepresented_sequences missing from S8_1.fq.gz
## Overrepresented_sequences missing from S8_2.fq.gz
## No overrepresented sequences were detected by FastQC

Session Information

R version 3.6.1 (2019-07-05)

Platform: x86_64-pc-linux-gnu (64-bit)

locale: LC_CTYPE=en_AU.UTF-8, LC_NUMERIC=C, LC_TIME=en_AU.UTF-8, LC_COLLATE=en_AU.UTF-8, LC_MONETARY=en_AU.UTF-8, LC_MESSAGES=en_AU.UTF-8, LC_PAPER=en_AU.UTF-8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=en_AU.UTF-8 and LC_IDENTIFICATION=C

attached base packages: parallel, stats, graphics, grDevices, utils, datasets, methods and base

other attached packages: readr(v.1.3.1), stringr(v.1.4.0), magrittr(v.1.5), scales(v.1.0.0), pander(v.0.6.3), kableExtra(v.1.1.0), dplyr(v.0.8.3), ngsReports(v.1.1.1), tibble(v.2.1.3), ggplot2(v.3.2.0) and BiocGenerics(v.0.30.0)

loaded via a namespace (and not attached): bitops(v.1.0-6), matrixStats(v.0.54.0), lubridate(v.1.7.4), webshot(v.0.5.1), RColorBrewer(v.1.1-2), httr(v.1.4.0), GenomeInfoDb(v.1.20.0), tools(v.3.6.1), backports(v.1.1.4), R6(v.2.4.0), lazyeval(v.0.2.2), colorspace(v.1.4-1), withr(v.2.1.2), tidyselect(v.0.2.5), compiler(v.3.6.1), rvest(v.0.3.4), Biobase(v.2.44.0), Cairo(v.1.5-10), xml2(v.1.2.0), DelayedArray(v.0.10.0), plotly(v.4.9.0), ggdendro(v.0.1-20), labeling(v.0.3), digest(v.0.6.20), Rsamtools(v.2.0.0), rmarkdown(v.1.14), XVector(v.0.24.0), pkgconfig(v.2.0.2), htmltools(v.0.3.6), highr(v.0.8), htmlwidgets(v.1.3), rlang(v.0.4.0), rstudioapi(v.0.10), shiny(v.1.3.2), zoo(v.1.8-6), hwriter(v.1.3.2), jsonlite(v.1.6), crosstalk(v.1.0.0), BiocParallel(v.1.18.0), RCurl(v.1.95-4.12), GenomeInfoDbData(v.1.2.1), Matrix(v.1.2-17), Rcpp(v.1.0.1), munsell(v.0.5.0), S4Vectors(v.0.22.0), stringi(v.1.4.3), yaml(v.2.2.0), MASS(v.7.3-51.4), SummarizedExperiment(v.1.14.0), zlibbioc(v.1.30.0), plyr(v.1.8.4), grid(v.3.6.1), promises(v.1.0.1), crayon(v.1.3.4), lattice(v.0.20-38), Biostrings(v.2.52.0), hms(v.0.5.0), zeallot(v.0.1.0), knitr(v.1.23), pillar(v.1.4.2), GenomicRanges(v.1.36.0), reshape2(v.1.4.3), stats4(v.3.6.1), glue(v.1.3.1), evaluate(v.0.14), ShortRead(v.1.42.0), latticeExtra(v.0.6-28), data.table(v.1.12.2), vctrs(v.0.2.0), httpuv(v.1.5.1), gtable(v.0.3.0), purrr(v.0.3.2), tidyr(v.0.8.3), assertthat(v.0.2.1), xfun(v.0.8), mime(v.0.7), xtable(v.1.8-4), later(v.0.8.0), viridisLite(v.0.3.0), truncnorm(v.1.0-8), GenomicAlignments(v.1.20.1) and IRanges(v.2.18.1)